Philipp Bucher

62 papers A 3C 3Journal 53Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Codes across (life)sciences. Biosyst. Robert Prinz, Philipp Bucher, Ádám Kun, Omar Paredes, Anna Aragno, Candice Shelby, Markus Gumbel, Elena Fimmel, Lutz Strüngmann
2024	J	`jnl`	ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements. Bioinform. Orit Adato, Anna Sloutskin, Hodaya Komemi, Ian Brabb, Sascha Duttke, Philipp Bucher, Ron Unger, Tamar Juven-Gershon
2021	J	`jnl`	Computational identification and experimental characterization of preferred downstream positions in human core promoters. PLoS Comput. Biol. René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon
2020	J	`jnl`	EPD in 2020: enhanced data visualization and extension to ncRNA promoters. Nucleic Acids Res. Patrick Meylan, René Dreos, Giovanna Ambrosini, Romain Groux, Philipp Bucher
2019	J	`jnl`	SPar-K: a method to partition NGS signal data. Bioinform. Romain Groux, Philipp Bucher
2018	J	`jnl`	MGA repository: a curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res. René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher
2018	J	`jnl`	PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. Bioinform. Giovanna Ambrosini, Romain Groux, Philipp Bucher
2017	J	`jnl`	SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. Nucleic Acids Res. Sunil Kumar, Giovanna Ambrosini, Philipp Bucher
2017	J	`jnl`	The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. Nucleic Acids Res. René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher
2016	J	`jnl`	A maximum-likelihood approach for building cell-type trees by lifting. BMC Genom. Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret
2016	J	`jnl`	Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. PLoS Comput. Biol. René Dreos, Giovanna Ambrosini, Philipp Bucher
2016	J	`jnl`	Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinform. Sunil Kumar, Philipp Bucher
2015	J	`jnl`	The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. Nucleic Acids Res. René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher
2014	J	`jnl`	Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res. Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic B. Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek, Olivier Michielin, Patricia M. Palagi, Jacques Rougemont, Torsten Schwede, Christian von Mering, Erik van Nimwegen, Daniel Walther, Ioannis Xenarios, Mihaela Zavolan, Evgeny M. Zdobnov, Vincent Zoete, Ron D. Appel
2014	—	`conf`	Principles of ChIP-seq Data Analysis Illustrated with Examples. IWBBIO Giovanna Ambrosini, René Dreos, Philipp Bucher
2014	J	`jnl`	Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. Bioinform. Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher
2014	J	`jnl`	Study of cell differentiation by phylogenetic analysis using histone modification data. BMC Bioinform. Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret
2014	—	`conf`	Transcription factor binding and nucleosome positioning are alternative pathways for transcription start site selection in eukaryotic promoters. IWBBIO René Dreos, Giovanna Ambrosini, Philipp Bucher
2013	J	`jnl`	EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res. René Dreos, Giovanna Ambrosini, Rouaïda Cavin Périer, Philipp Bucher
2013	C	`conf`	Phylogenetic Analysis of Cell Types Using Histone Modifications. WABI Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret
2013	J	`jnl`	UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res. Slavica Dimitrieva, Philipp Bucher
2012	J	`jnl`	Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinform. Slavica Dimitrieva, Philipp Bucher
2012	J	`jnl`	Practicality and Time Complexity of a Sparsified RNA Folding Algorithm. J. Bioinform. Comput. Biol. Slavica Dimitrieva, Philipp Bucher
2011	J	`jnl`	ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinform. Thomas J. Cradick, Giovanna Ambrosini, Christian Iseli, Philipp Bucher, Anton P. McCaffrey
2009	J	`jnl`	CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res. Viviane Praz, Philipp Bucher
2007	J	`jnl`	MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res. Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, Mauro Delorenzi
2007	J	`jnl`	Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinform. Davide Rambaldi, Barbara Felice, Viviane Praz, Philipp Bucher, Davide Cittaro, Alessandro Guffanti
2006	C	`ed.`	Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings WABI Philipp Bucher, Bernard M. E. Moret
2006	J	`jnl`	EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res. Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher
2006	J	`jnl`	HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. Nucleic Acids Res. Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher
2005	J	`jnl`	Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinform. Florence Armand, Philipp Bucher, C. Victor Jongeneel, Edward E. Farmer
2005	J	`jnl`	Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense. PLoS Comput. Biol. Peter Sperisen, Christoph D. Schmid, Philipp Bucher, Olav Zilian
2004	J	`jnl`	CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. Nucleic Acids Res. Viviane Praz, Vidhya Jagannathan, Philipp Bucher
2004	J	`jnl`	Recent improvements to the PROSITE database. Nucleic Acids Res. Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch
2004	J	`jnl`	The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res. Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, Philipp Bucher
2004	J	`jnl`	trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res. Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel
2003	—	`conf`	APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. ISMB (Supplement of Bioinformatics) Orla O'Sullivan, Mark Zehnder, Desmond G. Higgins, Philipp Bucher, Aurélien Grosdidier, Cédric Notredame
2003	C	`conf`	Modeling sequencing errors by combining Hidden Markov models. ECCB Claudio Lottaz, Christian Iseli, C. Victor Jongeneel, Philipp Bucher
2003	J	`jnl`	Signal search analysis server. Nucleic Acids Res. Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, Philipp Bucher
2003	J	`jnl`	The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov
2002	J	`jnl`	InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites Briefings Bioinform. Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist
2002	J	`jnl`	PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors. Briefings Bioinform. Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher
2002	J	`jnl`	The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res. Viviane Praz, Rouaïda Périer, Claude Bonnard, Philipp Bucher
2002	J	`jnl`	The PROSITE database, its status in 2002. Nucleic Acids Res. Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch
2001	J	`jnl`	The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov
2001	J	`jnl`	mmsearch: a motif arrangement language and search program. Bioinform. Thomas Junier, Marco Pagni, Philipp Bucher
2001	J	`jnl`	trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res. Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher
2000	J	`jnl`	InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinform. Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov
2000	J	`jnl`	The Eukaryotic Promoter Database (EPD). Nucleic Acids Res. Rouaïda Cavin Périer, Viviane Praz, Thomas Junier, Claude Bonnard, Philipp Bucher
1999	A	`conf`	ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences. ISMB Christian Iseli, C. Victor Jongeneel, Philipp Bucher
1999	J	`jnl`	The Eukaryotic Promoter Database (EPD): recent developments. Nucleic Acids Res. Rouaïda Périer, Thomas Junier, Claude Bonnard, Philipp Bucher
1999	J	`jnl`	The PROSITE database, its status in 1999. Nucleic Acids Res. Kay Hofmann, Philipp Bucher, Laurent Falquet, Amos Bairoch
1998	J	`jnl`	Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. Silico Biol. Emmanuelle Roulet, Igor Fisch, Thomas Junier, Philipp Bucher, Nicolas Mermod
1998	J	`jnl`	SEView: a Java applet for browsing molecular sequence data. Silico Biol. Thomas Junier, Philipp Bucher
1998	J	`jnl`	The Eukaryotic Promoter Database EPD. Nucleic Acids Res. Rouaïda Périer, Thomas Junier, Philipp Bucher
1997	J	`jnl`	The PROSITE database, its status in 1997. Nucleic Acids Res. Amos Bairoch, Philipp Bucher, Kay Hofmann
1996	J	`jnl`	A Flexible Motif Search Technique Based on Generalized Profiles. Comput. Chem. Philipp Bucher, Kevin Karplus, Nicolas Moeri, Kay Hofmann
1996	A	`conf`	A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System. ISMB Philipp Bucher, Kay Hofmann
1996	J	`jnl`	Computational analysis of transcriptional regulatory elements: a field in flux. Comput. Appl. Biosci. Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou
1996	J	`jnl`	The PROSITE database, its status in 1995. Nucleic Acids Res. Amos Bairoch, Philipp Bucher, Kay Hofmann
1994	A	`conf`	A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation. ISMB Philipp Bucher, Amos Bairoch
1984	J	`jnl`	Signal search analysis: a new method to localize and characterize functionally important DNA sequences. Nucleic Acids Res. Philipp Bucher, B. Bryan